QTL mapping and transcriptome profiling reveals that both target-site resistance and increased detoxification confer resistance to the pyrethroid bifenthrin in the spider mite Tetranychus urticae

This project investigated bifenthrin resistance in the two-spotted spider mite Tetranychus urticae. Bulked segregant analysis (BSA) based QTL-mapping experiments with the pyrethroid resistant strain MR-VLi were performed to identify genomic loci (QTLs) underlying bifenthrin resistance. Moreover, this project also aimed to investigate gene expression changes associated with pyrethroid resistance via differential gene expression analysis on a panel of bifenthrin resistant and susceptible strains (ES1, ROS-IT, UK4, IT3, RO1, MR-VL and El Juan). The analysis was based on (partially new) RNAseq data and genomic DNAseq data released to NCBI under accessions  PRJNA896577 and PRJNA895330 respectively. Datasets released here include Data S1: genomic VCF (gzipped) used as input for the RUN_BSA1.02.py script available at https://github.com/rmclarklab/BSA (Kurlovs et al. 2019, PMID: 31499416). Data S2: raw RNA-seq read counts on a per-gene basis for the strains ES1, ROS-IT, UK4, IT3, RO1, MR-VL and El Juan with 4 replicates for each strain.   

File S3: commands used for running BSA mapping script. Data S4: raw output of BSA mapping script